Background Pediatric migraine is a primary headache affecting daily activities and causing significant disability among children. However, clarity on the usage of prophylactic medications in children is yet to be established. This study was conducted with the aim of comparing the efficacy and safety of flunarizine and propranolol in the prophylaxis of pediatric migraine. Methodology An open-label randomized trial with parallel group assignment was conducted in the Department of Pediatrics of a tertiary care hospital in Northern India among patients aged five to 14 years with migraine having Pediatric Migraine Disability Assessment (PedMIDAS) score of 11 to 139 and a headache frequency of four or more days over a baseline period of 28 days. Enrolled patients were assigned randomly to receive either flunarizine (5 mg/day HS for the first month and then 10 mg/day HS for the next two months) or propranolol (1 mg/kg/day in two divided doses for three months) and then followed up monthly for three months for outcomes. The primary outcome was the proportion of children with a 50% or more reduction in the number of headache days compared to the 28-day baseline period with the last 28 days of the 12-week trial period. Secondary outcomes were headache-related disability (as measured by the absolute change in PedMIDAS score), the absolute change in the number of headache days, and the proportion and nature of adverse effects in the two groups. Results A total of 40 patients underwent randomization (20 in each group). Baseline parameters were comparable in the two groups. The primary outcome, that is, a 50% or more reduction in the number of headache days, was achieved in 10 out of 20 (50%) patients in the flunarizine group and 11 out of 20 (55%) patients in the propranolol group (p = 0.752). Both groups were comparable in terms of the primary outcome. There were also no significant between-group differences in terms of headache-related disability (change in PedMIDAS: 8.2 ± 2.97 in the flunarizine group vs 8.7 ± 3.95 in the propranolol group, p = 0.924) and absolute reduction in the number of headache days (4.3 ± 2.36 in the flunarizine group vs 4.3 ± 2.11 in the propranolol group, p = 0.989). Minor adverse effects like nausea, vomiting, drowsiness, and fatigue were comparable in the two groups. None of the patients reported any serious adverse events. Conclusion Flunarizine is as effective as propranolol for the prophylactic management of children with migraine. Both drugs were well-tolerated and safe.